Runs of Homozygosity Preliminary Investigation in Pig Breeds
Runs of homozygosity (ROH) are contiguous homozygous genomic segments that provide valuable insights into population history, selection pressures, and inbreeding levels. However, the global distribution of ROH and their implications for pig domestication and breeding are not yet fully understood. In...
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MDPI AG
2025-03-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/15/7/988 |
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| author | Yuqiang Liu Guangzhen Li Wondossen Ayalew Zhanming Zhong Xiaohong Liu Jiajie Sun Jiaqi Li |
| author_facet | Yuqiang Liu Guangzhen Li Wondossen Ayalew Zhanming Zhong Xiaohong Liu Jiajie Sun Jiaqi Li |
| author_sort | Yuqiang Liu |
| collection | DOAJ |
| description | Runs of homozygosity (ROH) are contiguous homozygous genomic segments that provide valuable insights into population history, selection pressures, and inbreeding levels. However, the global distribution of ROH and their implications for pig domestication and breeding are not yet fully understood. In this study, we analyzed whole-genome resequencing data from 1203 pigs across 49 breeds to characterize ROH patterns worldwide. European commercial pigs exhibited longer and more numerous ROH segments than Asian indigenous breeds, indicative of stronger artificial selection and higher inbreeding. Crossbreeding led to a reduction in ROH burden, with greater reductions observed when parental genetic divergence was larger. Notably, Asian and European pigs displayed distinct ROH islands, reflecting divergent selection pressures. Functional analysis revealed that these ROH islands were associated with growth, immunity, and reproduction. These findings enhance our understanding of the genetic diversity and selection history of global pig populations, providing valuable insights for future breeding strategies. |
| format | Article |
| id | doaj-art-74e5dac5ba8e4702a5233a96fc7d4208 |
| institution | DOAJ |
| issn | 2076-2615 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj-art-74e5dac5ba8e4702a5233a96fc7d42082025-08-20T03:06:27ZengMDPI AGAnimals2076-26152025-03-0115798810.3390/ani15070988Runs of Homozygosity Preliminary Investigation in Pig BreedsYuqiang Liu0Guangzhen Li1Wondossen Ayalew2Zhanming Zhong3Xiaohong Liu4Jiajie Sun5Jiaqi Li6State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, ChinaState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaState Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaRuns of homozygosity (ROH) are contiguous homozygous genomic segments that provide valuable insights into population history, selection pressures, and inbreeding levels. However, the global distribution of ROH and their implications for pig domestication and breeding are not yet fully understood. In this study, we analyzed whole-genome resequencing data from 1203 pigs across 49 breeds to characterize ROH patterns worldwide. European commercial pigs exhibited longer and more numerous ROH segments than Asian indigenous breeds, indicative of stronger artificial selection and higher inbreeding. Crossbreeding led to a reduction in ROH burden, with greater reductions observed when parental genetic divergence was larger. Notably, Asian and European pigs displayed distinct ROH islands, reflecting divergent selection pressures. Functional analysis revealed that these ROH islands were associated with growth, immunity, and reproduction. These findings enhance our understanding of the genetic diversity and selection history of global pig populations, providing valuable insights for future breeding strategies.https://www.mdpi.com/2076-2615/15/7/988breeding strategiescrossbreeding effectsdomesticationgenetic diversity |
| spellingShingle | Yuqiang Liu Guangzhen Li Wondossen Ayalew Zhanming Zhong Xiaohong Liu Jiajie Sun Jiaqi Li Runs of Homozygosity Preliminary Investigation in Pig Breeds Animals breeding strategies crossbreeding effects domestication genetic diversity |
| title | Runs of Homozygosity Preliminary Investigation in Pig Breeds |
| title_full | Runs of Homozygosity Preliminary Investigation in Pig Breeds |
| title_fullStr | Runs of Homozygosity Preliminary Investigation in Pig Breeds |
| title_full_unstemmed | Runs of Homozygosity Preliminary Investigation in Pig Breeds |
| title_short | Runs of Homozygosity Preliminary Investigation in Pig Breeds |
| title_sort | runs of homozygosity preliminary investigation in pig breeds |
| topic | breeding strategies crossbreeding effects domestication genetic diversity |
| url | https://www.mdpi.com/2076-2615/15/7/988 |
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